A group called the Shinkansen Ultra Evolution Institute was investigating a recent rash of monster attacks happening in Japan after the appearance of a mysterious Black Shinkansen. The SUEI had a major weapon for the fight - Shinkalions, bullet trains that can transform into giant mecha. One boy, Hayato Hayasugi, was a huge fan of trains and stumbled upon his father’s secret work for the SUEI. Surprisingly, Hayato soon became a Shinkalion driver! As perhaps Japan’s best chance of survival, Hayato and other kids take on the great responsibility of fighting otherworldly enemies.

Now, a new giant enemy has come from space looking to conquer the planet. Although the SUEI have a new prototype Shinkalion known as the ALFA-X to take up the fight, Hayato’s father, Hokuto, disappears. A 9-year-old version of Hokuto leaps through time to the present to help fight the alien attackers and drives the ALFA-X!